Search Results (7,119)

The application of slow-release nitrogen fertilizer not only economizes labor input, but also decreases the frequency of use of mechanical intakes, with significant implications in advancing modern intensive agricultural production. Whether slow-release nitrogen fertilizer application can influence the association between microbial diversity and soil multifunctionality remains controversial. This study analyzed the spatial variances of soil environmental factors, soil multifunctionality, and their correlations with bacterial and fungal communities under five nitrogen application rates. The key factors influencing the dominant microbial species and community structures at different spatial locations were determined by the slow-release nitrogen fertilizer application rate, and the driving factors and dominant species of soil multifunctionality were identified. In contrast to the control group, moderate slow-release nitrogen fertilizer application enhanced soil multifunctionality and ameliorated the resilience of microbial diversity loss at diverse spatial locations resulting from irrational nitrogen fertilizer application. The resilience of the fungal community to disturbances caused by fertilization was lower than that of the bacterial community. Bacterial diversity exhibited a significant correlation with soil multifunctionality, and the soil multifunctionality intensity under 240 kg ha⁻¹ treatment increased by 159.01% compared to the CK. The main dominant bacterial communities and the dominant fungal community Ascomycota affected soil multifunctionality through slow-release nitrogen fertilizer application. Structural equation modeling and random forest analysis demonstrated that bacterial community diversity, particularly in bulk soil and the rhizosphere, community composition, and soil nitrogen form are the primary driving factors of soil multifunctionality. Results indicated that the microbial niche alterations induced by slow-release nitrogen fertilizer application positively affect soil multifunctionality. Full article

The cultivation of Fritillaria ussuriensis faces challenges due to the prevalent Fritillaria wilt disease, hindering large-scale production. To address this, we aimed to understand the disease’s characteristics and develop effective prevention measures. Microbial communities of diseased F. ussuriensis plants were analyzed, pathogenic and antagonistic strains were screened, and biocontrol feasibility was tested. We identified Botryotinia predominance in aboveground parts and variations in Mrakia, Humicola, llyonectria, and Fusarium in underground parts. The pathogens Fusarium oxysporum IFM-1 and Fusarium solani IFM-52 isolated from diseased F. ussuriensis not only caused severe Fritillaria wilt but were also pathogenic to Lilium lancifolium and Allium cepa var. aggregatum in Liliaceae. The antagonistic Bacillus tequilensis LFM-30 and Trichoderma koningiopsis IFM-47 isolated from diseased plants significantly alleviated plant wilt and showed promise in preventing wilt disease caused by Fusarium in Liliaceae plants. Our study highlights distinct microbial differences between healthy and diseased F. ussuriensis and underscores the pathogenicity of Fusarium. Using T. koningiopsis and B. tequilensis either singly or in combination could offer effective biocontrol against F. solani and F. oxysporum, benefiting F. ussuriensis and related Liliaceae plants. Full article

Kiwifruit Vine Decline Syndrome (KVDS) has become a major concern in Italy, impacting both plant health and production. This study aims to investigate how KVDS affects soil health indicators and the composition of soil microbial communities by comparing symptomatic and asymptomatic areas in two kiwifruit orchards located in Latium, Italy. Soil samples were collected during both spring and autumn to assess seasonal variations in soil physicochemical properties, enzyme activities, and microbial biomass. The results reveal that KVDS influences several soil properties, including pH, electrical conductivity, and the contents of water-soluble carbon and nitrogen. However, these effects varied between orchards and across different seasons. Additionally, KVDS significantly impacts soil enzyme activities and microbial biomass, as assessed through the phospholipid fatty acid (PLFA) analysis, particularly showing an increase in fungal biomass in symptomatic areas. Metabarcoding further demonstrates that microbial communities differ between symptomatic and asymptomatic soils, exhibiting notable shifts in both diversity and relative abundance. Our findings emphasise the complex interactions between plants, soil, and microbial communities in relation to KVDS. This suggests that the syndrome is multifactorial and likely linked to an imbalance in soil microbial communities at the rhizosphere level, which can negatively affect soil health. Full article

Paddy fields are important anthropogenic emission sources of methane (CH₄). However, it is not clear how rice root development and rhizosphere soil properties affect CH₄ emissions. Therefore, we selected rice varieties with similar growth periods but different root traits in the local area. We measured CH₄ emission fluxes, cumulative CH₄ emissions, root dry weight, root length, and the dissolved organic carbon (DOC), microbial biomass carbon (MBC), redox potential (Eh), ammonium nitrogen (NH+ 4–N), and nitrate nitrogen (NO− 3–N) contents in rhizosphere soil. Methanogens and methanotrophs are crucial factors influencing CH₄ emissions; thus, their abundance and community composition were also assessed. The result showed that CH₄ fluxes of each rice variety reached the peak at tillering stage and jointing-booting stage. The CH₄ emissions in tillering stage were the largest in each growth period. CH₄ emissions had negative correlations with root length, root dry weight, Eh NO− 3–N, methanotroph abundance, and the pmoA/mcrA ratio, and positive correlations with NH+ 4–N, MBC, DOC, and methanogen abundance. Path analysis confirmed methanogens and methanotrophs as direct influences on CH₄ emissions. Root development and rhizosphere soil properties affect CH₄ emissions indirectly through these microbes. This study suggests that choosing rice varieties with good root systems and managing the rhizosphere soil can effectively reduce CH₄ emissions. Full article

Background: Phenylketonuria (PKU) is a metabolic disorder that necessitates dietary restrictions, potentially impacting the composition of gut and oral microbiota. This study aimed to compare the microbiota composition between children with PKU and healthy controls. Methods: Using 16S rRNA gene sequencing, we analysed microbial communities at six phylogenetic levels. Results: Our findings revealed significant differences in the gut microbiota: Euryarchaeota was more abundant in controls (p = 0.01), while Bacilli and Lactobacillales were higher in PKU children (p = 0.019). Methanobacteriales were significantly elevated in controls (p = 0.01). At the genus and species levels, PKU children had higher Streptococcus and Eubacterium dolichum (p = 0.019, p = 0.015), whereas controls had more Barnesiella, Coprococcus, and Faecalibacterium prausnitzii (p = 0.014, p = 0.019, p = 0.014). In the oral microbiota, control children exhibited significantly higher Bacteroidetes (p = 0.032), while PKU children had increased Bacilli and Betaproteobacteria (p = 0.0079, p = 0.016). Streptococcus and Neisseria were more prevalent in PKU (p = 0.0079, p = 0.016). Conclusions: These results suggest that PKU and its dietary management significantly alter the gut and oral microbiota composition. Understanding these microbial shifts could have implications for managing PKU and improving patient outcomes. Full article

Microbial enhanced oil recovery (MEOR) is a promising technology for oil field extraction. This study investigated a co-culture system of Pseudomonas aeruginosa and Bacillus subtilis to increase MEOR efficacy. We analyzed bacterial growth, biosurfactant production, and crude oil emulsified performance under different inoculation ratios. Compared to single cultures, the co-culture system showed superior growth and functional expression, with an optimal inoculation ratio of 1:1. Quantitative assessments of the cell numbers and biosurfactant production during the co-culture revealed that rapid B. subtilis proliferation in early stages significantly stimulated P. aeruginosa growth. This interaction increased cell density and rhamnolipid production by 208.05% and 216.25%, respectively. The microscopic etching model displacement results demonstrated enhanced emulsification and mobilization of crude oil by the co-culture system, resulting in 94.48% recovery. A successful field application in a block-scale reservoir increased cumulative oil production by 3.25 × 10³ t. An analysis of microbial community structure and function in different phases revealed that after co-culture system injection, Pseudomonas became the dominant genus in the reservoir community, with an average abundance of 24.80%. Additionally, the abundance of biosurfactant-producing and hydrocarbon-degrading bacteria increased significantly. This research and the application of the P. aeruginosa and B. subtilis co-culture system provide novel insights and strategies for MEOR. Full article

We studied the microbial diversity colonizing limestone rock pools at a Neolithic Monument (Arbor Low, Derbyshire, England). Five pools were analyzed: four located at the megaliths of the stone circle and one pool placed at the megalith at the Gib Hill burial mound 300 m distant. Samples were taken from rock pool walls and sediments, and investigated through molecular metabarcoding. The microbiome consisted of 23 phyla of bacteria (831 OTUs), 4 phyla of archaea (19 OTUs), and 27 phyla of microbial eukarya (596 OTUs). For bacteria, there were statistically significant differences in wall versus sediment populations, but not between pools. For archaea and eukarya, significant differences were found only between pools. The most abundant bacterial phylum in walls was Cyanobacteriota, and Pseudomonadota in sediments. For archaea and microbial eukarya, the dominant phyla were Euryarcheota and Chlorophyta, respectively, in both wall and sediments. The distant pool (P5) showed a markedly different community structure in phyla and species, habitat discrimination, and CHN content. Species sorting and dispersal limitation are discussed as mechanisms structuring the microbiome assemblages and their spatial connectivity. The Arbor Low microbiome is composed of terrestrial representatives common in extreme environments. The high presence of Cyanobacteriota and Chlorophyta in the Arbor Low stones is troubling, as these microorganisms can induce mechanical disruption by penetrating the limestone matrix through endolithic/chasmoendolithic growth. Future research should focus on the metabolic traits of strains to ascertain their implication in bioweathering and/or biomineralization. Full article

The production of wheat is fundamentally interconnected with worldwide food security. The practice of deep tillage (DT) cultivation has shown advantages in terms of soil enhancement and the mitigation of diseases and weed abundance. Nevertheless, the specific mechanisms behind these advantages are unclear. Accordingly, we aimed to clarify the influence of DT on rhizosphere soil (RS) microbial communities and its possible contribution to the improvement of soil quality. Soil fertility was evaluated by analyzing several soil characteristics. High-throughput sequencing techniques were utilized to explore the structure and function of rhizosphere microbial communities. Despite lowered fertility levels in the 0–20 cm DT soil layer, significant variations were noted in the microbial composition of the DT wheat rhizosphere, with Acidobacteria and Proteobacteria being the most prominent. Furthermore, the abundance of Bradyrhizobacteria, a nitrogen-fixing bacteria within the Proteobacteria phylum, was significantly increased. A significant increase in glycoside hydrolases within the DT group was observed, in addition to higher abundances of amino acid and carbohydrate metabolism genes in the COG and KEGG databases. Moreover, DT can enhance soil quality and boost crop productivity by modulating soil microorganisms’ carbon and nitrogen fixation capacities. Full article

Forests play a key role in the global carbon (C) cycle through multiple interactions between above-ground and soil microbial communities. Deeper insights into the soil microbial composition and diversity at different spatial scales and soil depths are of paramount importance. We hypothesized that in a homogeneous above-ground tree cover, the heterogeneous distribution of soil microbial functional diversity and processes at the small scale is correlated with the soil’s chemical properties. From this perspective, in a typical Mediterranean holm oak (Quercus ilex L.) peri-urban forest, soil carbon dioxide (CO₂) emissions were measured with soil chambers in three different plots. In each plot, to test the linkage between above-ground and below-ground communities, soil was randomly sampled along six vertical transects (0–100 cm) to investigate soil physico-chemical parameters; microbial processes, measured using Barometric Process Separation (BaPS); and structural and functional diversity, assessed using T-RFLP and qPCR Real Time analyses. The results highlighted that the high spatial variability of CO₂ emissions—confirmed by the BaPS analysis—was associated with the microbial communities’ abundance (dominated by bacteria) and structural diversity (decreasing with soil depth), measured by H′ index. Bacteria showed higher variability than fungi and archaea at all depths examined. Such an insight showed the clear ecological and environmental implications of soil in the overall sustainability of the peri-urban forest system. Full article

The use of non-degradable plastic mulch has become an essential agricultural practice for increasing crop yields, but continued use has led to contamination problems and in some cropping areas decreases in agricultural productivity. The subsequent emergence of biodegradable plastic mulches is a technological solution to these issues, so it is important to understand how different soil characteristics and field management strategies will affect the rate at which these new materials degrade in nature. In this work, a series of lab-scale hydrolytic degradation experiments were conducted to determine how different soil characteristics (type, pH, microbial community composition, and particle size) affected the degradation rate of a sprayable polyester–urethane–urea (PEUU) developed as a biodegradable mulch. The laboratory experiments were coupled with long-term, outdoor, soil degradation studies, carried out in Clayton, Victoria, to build a picture of important factors that can control the rate of PEUU degradation. It was found that temperature and acidity were the most important factors, with increasing temperature and decreasing pH leading to faster degradation. Other important factors affecting the rate of degradation were the composition of the soil microbial community, the mass loading of PEUU on soil, and the degree to which the PEUU was in contact with the soil. Full article

Recent advances in microbiome research have uncovered a dynamic and complex connection between the gut and lungs, known as the gut–lung axis. This bidirectional communication network plays a critical role in modulating immune responses and maintaining respiratory health. Mediated by immune interactions, metabolic byproducts, and microbial communities in both organs, this axis demonstrates how gut-derived signals, such as metabolites and immune modulators, can reach the lung tissue via systemic circulation, influencing respiratory function and disease susceptibility. To explore the implications of this connection, we conducted a systematic review of studies published between 2001 and 2024 (with as much as nearly 60% covering the period 2020–2024), using keywords such as “gut–lung axis”, “microbiome”, “respiratory disease”, and “immune signaling”. Studies were selected based on their relevance to gut–lung communication mechanisms, the impact of dysbiosis, and the role of the gut microbiota in respiratory diseases. This review provides a comprehensive overview of the gut–lung microbiome axis, emphasizing its importance in regulating inflammatory and immune responses linked to respiratory health. Understanding this intricate pathway opens new avenues for microbiota-targeted therapeutic strategies, which could offer promising interventions for respiratory diseases like asthma, chronic obstructive pulmonary disease, and even infections. The insights gained through this research underscore the potential of the gut–lung axis as a novel target for preventative and therapeutic approaches in respiratory medicine, with implications for enhancing both gut and lung health. Full article

Due to the growing focus on daily hygiene practices, sodium dodecyl sulfate (SDS), a widely used surfactant, is increasingly found in domestic sewage and rainfall runoff. Upon entering the lake–terrestrial ecotone, SDS affects the composition, abundance, and functional capacity of soil bacterial communities due to its bacteriostatic properties. To investigate the effects of long-term discharge of sewage containing low concentrations of SDS on microorganisms in the lake–terrestrial ecotone, alterations in bacterial community structure, functional genes, and biomass were examined using a simulated continuous pollutant input. The results indicated the following: (1) The degradation rate of sodium dodecyl sulfate (SDS) by soil microorganisms in the lake–terrestrial ecotone under long-term and low concentrations of SDS stress ranged from 11 to 16 mg/kg·d. (2) The effects of low concentrations and long-term SDS stress on bacterial community structure and gene function in the lake–terrestrial ecotone differed significantly from those of short-term pollution. The damage to microbial-promoted material cycling in the lake–terrestrial ecotone was more severe; however, the proliferation of pathogenic bacteria remained continuously suppressed. (3) Soil bacteria in the lake–terrestrial ecotone responded to the stress of long-term and low concentrations of SDS primarily by enhancing chemotaxis and tolerance. Full article

This study investigates gender-based differences in the gut microbiota of Simmental cattle, focusing on bacterial, archaeal, and fungal communities. Fecal samples were collected and analyzed using high-throughput sequencing, with taxonomic classification performed through the SILVA and UNITE databases. Alpha and beta diversity metrics were assessed, revealing significant differences in the diversity and composition of archaeal communities between males and females. Notably, females exhibited higher alpha diversity in archaea, while beta diversity analyses indicated distinct clustering of bacterial and archaeal communities by gender. The study also identified correlations between specific microbial taxa and hematological parameters, with Treponema and Methanosphaera showing gender-specific associations that may influence cattle health and productivity. These findings highlight the importance of considering gender in microbiota-related research and suggest that gender-specific management strategies could optimize livestock performance. Future research should explore the role of sex hormones in shaping these microbial differences. Full article

Phosphorus is crucial for plant growth and development, but excess fertilizer not absorbed by plants often binds with metal ions like iron and manganese, forming insoluble compounds that contribute to soil environmental pollution. This study investigates the impact of Burkholderia sp., a phosphate-solubilizing bacterium utilized as a biofertilizer, on the fertility of T. grandis soil, alongside the associated shifts in soil metabolites and their relationship with microbial communities after inoculation. The soil microbial community structures and metabolite profiles were analyzed via amplicon sequencing and high-resolution untargeted metabolomics. The inoculation of phosphate-solubilizing bacteria led to a significant (p < 0.05) enhancement in total phosphorus, potassium, and nitrogen concentrations in the soil, with a marked increase in available phosphorus in bulk soil (p < 0.05). Moreover, the microbial community structure exhibited significant shifts, particularly in the abundance of bacterial phyla such as Acidobacteria, Chloroflexi, Proteobacteria, and the fungal phylum Ascomycota. Metabolomic analysis revealed distinct metabolites, including fatty acids, hormones, amino acids, and drug-related compounds. Key microbial taxa such as Chloroflexi, Proteobacteria, Acidobacteria, Verrucomicrobia, Mucoromycota, and Ascomycota indirectly contributed to soil phosphorus metabolism by influencing these differential metabolites. In conclusion, the application of phosphate-solubilizing bacteria offers an innovative approach to improving soil quality in T. grandis, promoting phosphorus utilization efficiency, and enhancing soil ecosystem health by optimizing microbial communities and metabolite compositions. Full article

The deep ocean harbors a group of highly diversified microbes, while our understanding of the active microbes that are real contributors to the nutrient cycle remains limited. In this study, we report eukaryotic and prokaryotic communities in ~590 m and 1130 m depths using 16S and 18S rRNA Illumina reads (miTags) extracted from 15 metagenomes (MG) and 14 metatranscriptomes (MT). The metagenomic 16S miTags revealed the dominance of Gammaproteobacteria, Alphaproteobacteria, and Nitrososphaeria, while the metatranscriptomic 16S miTags were highly occupied by Gammaproteobacteria, Acidimicrobiia, and SAR324. The consistency of the active taxa between the two depths suggests the homogeneity of the functional microbial groups across the two depths. The eukaryotic microbial communities revealed by the 18S miTags of the metagenomic data are dominated by Polycystinea; however, they were almost all absent in the 18S metatranscriptomic miTags. The active eukaryotes were represented by the Arthropoda class (at 590 m depth), Dinophyceae, and Ciliophora classes. Consistent eukaryotic communities were also exhibited by the 18S miTags of the metatranscriptomic data of the two depths. In terms of biodiversity, the ACE and Shannon indices of the 590 m depth calculated using the 18S metatranscriptomic miTags were much higher than those of the 1130 m depth, while a reverse trend was shown for the indices based on the metagenomic data. Our study reports the active microbiomes functioning in the nutrient utilization and carbon cycle in the deep-sea zone, casting light on the quantification of the ecological processes occurring in the deep ocean. Full article